For weeks and months, the 49ers have sent a crystal clear message with every move they’ve made involving Aldon Smith and his repeated troubles: If you’re valuable enough as a player, they’ll ignore just about anything.

It was only a few days ago that the NFL finally weighed on on Smith—a nine-game suspension, starting immediately—and the 49ers merely shrugged and offered no other tangible reaction.

Smith is a great player and he is the 49ers’ guy, most specifically he is GM Trent Baalke’s guy, and that’s that: Get ready for Game 10, Aldon!

So what will the 49ers reaction be to the early-morning arrest of defensive end Ray McDonald on suspicion of felony domestic-abuse? If they follow their pattern, assuming McDonald is judged to be valuable enough, the 49ers will do essentially nothing and let the league do whatever it will.

Because the 49ers have abdicated any oversight of their players’ conduct. Well, of their good players’ conduct.

The 49ers’ standard for behavior is… that they have no standard for behavior as long as the player can produce for them in the times when he is not otherwise banished from the league… and what we’re seeing is a bunch of players who have absolutely gotten that unspoken message and continue to do whatever the hell they want.

We’re seeing it. The 49ers are experiencing it. Now the NFL has to deal with it on a regular basis.

And that’s a bad, bad place to be for a franchise that tries to hold itself up as a model organization in all ways.

This also comes immediately after Commissioner Roger Goodell issued a tougher policy on dealing with players who commit domestic abuse, in the wake of the outcry over his meager two-game suspension of Ray Rice.

It’s unclear when the commissioner can or will issue penalties in these cases—is there a process? does he wait until the investigation is complete?—but it’s safe to say that, pending all other developments, McDonald could be looking at a six-game suspension pretty quickly.

We can all surmise that the 49ers and McDonald won’t get any benefit of the doubt in this case, nor should they.

If the facts show that McDonald struck his pregnant fiancee, then the legal system and the NFL will and should come down with full force. San Jose Police sergeant Heather Randol called me to emphasize that the police report on this case has not and probably will not be made public. All suggestions about what happened are from reporters on the story and her initial media release.

So where are the 49ers on all this? They bungled the Smith situation from Day 1 and now McDonald’s situation only magnifies the spotlight on 49ers owner Jed York, who has let the Smith situation continue to be bungled.

This, generally, is why I’ve been pounding the 49ers on Aldon Smith for months, just to hear if they have any standards for player conduct and to emphasize that the lack of such standards is a moral abandonment.

They never had an answer to any of this, by the way. And though I had the argument with Harbaugh about it, I really don’t put it on him—he’s the coach, his job is to win games.

It’s supposed to be up to the GM, president and the owner to carry out the larger view of a team’s behavior and the way it interacts with the community.

Which is where the 49ers have failed at an alarming clip of late. No team has had more players arrested in the last few years, and no team has acted less bothered by this than the 49ers.

Remember, Harbaugh and Baalke repeatedly emphasized Smith’s punishment was up to the league, not the 49ers. Remember, the 49ers rushed Smith back into the lineup two days after his DUI arrest last season and then right back in after his five-game rehab stint (for which he was paid every dollar of his salary by the 49ers).

They left it up to the league because the 49ers didn’t and wouldn’t discipline Smith themselves. Again: That’s an abandonment of principle.

Remember, Harbaugh said this in June 2013, specifically about the Seahawks’ run of PED issues, but he said the words and he can be held partially to them:

“We want to be a above reproach in everything and do everything by the rules.”

The 49ers have traveled a long way from “above reproach” in the behavior of some of their best players. They’ve gone so far that I don’t know if York can walk it back—he has allowed Baalke and Harbaugh to create a bandit atmosphere. If the players perform on the field, they’ve come to believe (with good reason) that they can do almost anything they want off of it.

That’s the message from 49ers management and Sunday morning was another reminder of it.

“Beyond the Headline” hosts and hold a wide-sweeping discussion about their experiences covering the devastating at the Ghost Ship warehouse that killed 36 people. They are joined by Bay Area News Group colleagues in award-winning investigative reporter , Oakland city beat reporter and seasoned photojournalist , who has the distinction of having been on scene for the Oakland’s two deadliest fires...